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Abstract Due to their large carbon storage capacity and ability to exchange subterranean CO₂with the atmosphere, soils are key components in the carbon balance in semi‐arid ecosystems. Most studies have focused on shallow (e.g., <30 cm depth) soil CO₂dynamics neglecting processes in deeper soil layers where highly CO₂‐enriched air can be stored or transported through soil pores and fissures. Here, we examine the relationship among variations in subterranean CO₂molar fraction, volumetric water content, soil temperature and atmospheric pressure during three years within soil profiles (0.15, 0.50, and 1.50 m depths) in two semi‐arid grasslands located in southeastern Spain. We applied a wavelet coherence analysis to study the temporal variability and temporal correlation between the CO₂molar fraction and its covariates (soil temperature, soil moisture and atmospheric pressure). Our results show that CO₂dynamics are strongly influenced by changes in atmospheric pressure from semidiurnal, diurnal and synoptic to monthly time‐scales for all soil depths. In contrast, only weak daily dependencies were found at the surface level (0.15 m) regarding soil temperature and volumetric water content. Atmospheric pressure changes substantially influence variations in the CO₂content (with daily fluctuations of up to 2000 ppm) denoting transportation through soil layers. These results provide insights into the importance of subterranean storage and non‐diffusive gas transport that could influence soil CO₂efflux rates, processes that are not considered when applying the flux‐gradient approach and, which can be especially important in ecosystems with high air permeability between the unsaturated porous media and the atmosphere.